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Comment: Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
3 months ago mat149 ▴ 80
1
vote
3
replies
431
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How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome BSgenomeForge
updated 3 months ago by 68k • written 3 months ago by ▴ 80
0
votes
0
replies
856
views
Comment: Comment: ISO a solution to rank-order introns by transcript
12 months ago mat149 ▴ 80
3
votes
3
replies
856
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
15 months ago • updated 12 months ago mat149 ▴ 80
3
votes
4
replies
986
views
Store output of matchPWM()
biostrings Biostrings
20 months ago • updated 19 months ago mat149 ▴ 80
1
vote
0
replies
986
views
Answer: Answer: Store output of matchPWM()
19 months ago mat149 ▴ 80
2
votes
1
reply
648
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 20 months ago by 43k • written 20 months ago by ▴ 80
0
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1
reply
986
views
Comment: Comment: Store output of matchPWM()
20 months ago mat149 ▴ 80
0
votes
0
replies
678
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
22 months ago mat149 ▴ 80
0
votes
1
reply
1.5k
views
Comment: Comment: Need help generating BSgenome and orgdb
23 months ago mat149 ▴ 80
2
votes
1
reply
913
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
23 months ago mat149 ▴ 80
2
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4
replies
1.5k
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
2.2 years ago • updated 23 months ago mat149 ▴ 80
0
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1
reply
1.9k
views
Comment: Comment: Help with orgdb for non-model species via makeOrgPackageFromNCBI
2.2 years ago mat149 ▴ 80
0
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1
reply
1.9k
views
Comment: Comment: Help with orgdb for non-model species via makeOrgPackageFromNCBI
2.2 years ago mat149 ▴ 80
2
votes
5
replies
1.9k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 80
1
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0
replies
1.8k
views
Comment: C: indexBam(), summarizeOverlaps() error: RNA-seq
6.9 years ago mat149 ▴ 80
2
votes
3
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1.8k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.9 years ago by ★ 6.6k • written 6.9 years ago by ▴ 80
1
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0
replies
7.0k
views
Comment: C: Using GenomicFeatures to extract the upstream and downstream region of a transcr
6.9 years ago mat149 ▴ 80
0
votes
0
replies
5.4k
views
Comment: C: How to calculate log2 fold change between two groups in a microarray study
6.9 years ago mat149 ▴ 80
6
votes
3
replies
5.4k
views
How to calculate log2 fold change between two groups in a microarray study
limma
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 80
0
votes
1
reply
1.5k
views
Making microarray probeset presence/absence calls
oligo
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 80
1
vote
0
replies
16k
views
Answer: A: Converting gene symbol list to Entrez IDs
7.9 years ago mat149 ▴ 80
4
votes
2
replies
2.2k
views
Help: extract counts from RNA-seq .bam/.bai files
counts edger
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 80
0
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0
replies
6.4k
views
Answer: A: Duplicate gene ID's returned from limma microarray analysis
9.0 years ago mat149 ▴ 80
5
votes
11
replies
6.4k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 3.7 years ago by 53k • written 9.0 years ago by ▴ 80
0
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1
reply
6.4k
views
Comment: C: Duplicate gene ID's returned from limma microarray analysis
9.0 years ago mat149 ▴ 80
0
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0
replies
1.4k
views
Comment: A: Probe sequences to Entrez Ids
9.0 years ago mat149 ▴ 80
0
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0
replies
1.7k
views
Comment: A: ISO help with goana
9.0 years ago mat149 ▴ 80
1
vote
5
replies
1.7k
views
ISO help with goana
limma
9.0 years ago mat149 ▴ 80
0
votes
1
reply
1.7k
views
Comment: C: ISO help with goana
9.0 years ago mat149 ▴ 80
0
votes
1
reply
2.7k
views
Comment: C: How to filter probesets from the expression set that do not contain Entrez/Gene
9.0 years ago mat149 ▴ 80
0
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4
replies
2.7k
views
How to filter probesets from the expression set that do not contain Entrez/Gene Symbol identifiers
oligo
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 80
0
votes
0
replies
5.5k
views
Comment: C: How to select the genes mapped to an enriched KEGG pathway (kegga)
9.0 years ago mat149 ▴ 80
0
votes
1
reply
946
views
ISO help making a heatmap from a subset of microarray probes in the expression set
oligo
updated 9.1 years ago by 68k • written 9.1 years ago by ▴ 80
0
votes
0
replies
5.5k
views
Comment: C: How to select the genes mapped to an enriched KEGG pathway (kegga)
9.1 years ago mat149 ▴ 80
0
votes
1
reply
5.5k
views
Comment: C: How to select the genes mapped to an enriched KEGG pathway (kegga)
9.1 years ago mat149 ▴ 80
0
votes
0
replies
3.9k
views
Comment: A: How to make a (limma) heatmap displaying gene ID's as rownames
9.1 years ago mat149 ▴ 80
4
votes
5
replies
3.9k
views
How to make a (limma) heatmap displaying gene ID's as rownames
limma microarray
9.1 years ago mat149 ▴ 80
0
votes
5
replies
5.5k
views
How to select the genes mapped to an enriched KEGG pathway (kegga)
kegga
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 80
0
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0
replies
2.5k
views
Comment: C: need help with microarray GO enrichment using goana
9.1 years ago mat149 ▴ 80
0
votes
1
reply
2.5k
views
Comment: C: need help with microarray GO enrichment using goana
9.1 years ago mat149 ▴ 80
0
votes
4
replies
2.5k
views
need help with microarray GO enrichment using goana
goana limma
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 80
0
votes
1
reply
1.2k
views
ISO help making a colored pathway diagram to display enriched KEGG pathways
limma edger
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 80
0
votes
2
replies
1.3k
views
Help with limma contrast/design matrices
limma contrast matrix
9.1 years ago mat149 ▴ 80
0
votes
0
replies
2.3k
views
Comment: C: Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zeb
9.2 years ago mat149 ▴ 80
0
votes
1
reply
2.3k
views
Comment: C: Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zeb
9.2 years ago mat149 ▴ 80
0
votes
1
reply
2.3k
views
Comment: C: Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zeb
9.2 years ago mat149 ▴ 80
2
votes
6
replies
2.3k
views
Help: obtain Entrez ID's from limma top table with Affymetrix microarray (pd.zebgene.1.1.st)
affmetrix microarray limma oligo
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 80
0
votes
2
replies
1.9k
views
Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 9.3 years ago by ★ 4.1k • written 9.3 years ago by ▴ 80
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